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Article|19 Apr 2023|OPEN
Two-step model of paleohexaploidy, ancestral genome reshuffling and plasticity of heat shock response in Asteraceae
Xiangming Kong1 ,† , Yan Zhang1 ,† , Ziying Wang1 ,† , Shoutong Bao1 ,† , Yishan Feng1 , Jiaqi Wang1 , Zijian Yu1 , Feng Long1 , Zejia Xiao1 , Yanan Hao1 , Xintong Gao1 , Yinfeng Li1 , Yue Ding1 , Jianyu Wang1 , Tianyu Lei1,2,3 , , Chuanyuan Xu1 , , Jinpeng Wang,1,2,3 ,
1Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
2State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
3University of Chinese Academy of Sciences, Beijing 100049, China
*Corresponding author. E-mail: leitianyu@ncst.edu.cn,xuchuanyuan@ncst.edu.cn,wangjinpeng@ibcas.ac.cn
Xiangming Kong,Yan Zhang,Ziying Wang and Shoutong Bao contributed equally to the study.

Horticulture Research 10,
Article number: uhad073 (2023)
doi: https://doi.org/10.1093/hr/uhad073
Views: 243

Received: 20 Jan 2023
Accepted: 10 Apr 2023
Published online: 19 Apr 2023

Abstract

An ancient hexaploidization event in the most but not all Asteraceae plants, may have been responsible for shaping the genomes of many horticultural, ornamental, and medicinal plants that promoting the prosperity of the largest angiosperm family on the earth. However, the duplication process of this hexaploidy, as well as the genomic and phenotypic diversity of extant Asteraceae plants caused by paleogenome reorganization, are still poorly understood. We analyzed 11 genomes from 10 genera in Asteraceae, and redated the Asteraceae common hexaploidization (ACH) event ~70.7–78.6 million years ago (Mya) and the Asteroideae specific tetraploidization (AST) event ~41.6–46.2 Mya. Moreover, we identified the genomic homologies generated from the ACH, AST and speciation events, and constructed a multiple genome alignment framework for Asteraceae. Subsequently, we revealed biased fractionations between the paleopolyploidization produced subgenomes, suggesting the ACH and AST both are allopolyplodization events. Interestingly, the paleochromosome reshuffling traces provided clear evidence for the two-step duplications of ACH event in Asteraceae. Furthermore, we reconstructed ancestral Asteraceae karyotype (AAK) that has 9 paleochromosomes, and revealed a highly flexible reshuffling of Asteraceae paleogenome. Of specific significance, we explored the genetic diversity of Heat Shock Transcription Factors (Hsfs) associated with recursive whole-genome polyploidizations, gene duplications, and paleogenome reshuffling, and revealed that the expansion of Hsfs gene families enable heat shock plasticity during the genome evolution of Asteraceae. Our study provides insights on polyploidy and paleogenome remodeling for the successful establishment of Asteraceae, and is helpful for further communication and exploration of the diversification of plant families and phenotypes.